RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

Pathophysiology of Acute Kidney Frailty.

Acute kidney frailty is a premorbid condition of diminished renal functional reserve that predisposes to acute kidney injury; this condition results from subclinical wear or distortion of renal homeostatic responses that protect the renal excretory function. Knowledge of its pathophysiological basis is critical for the development of diagnostic and therapeutic strategies that allow for prophylactic intervention and disease prevention.

Kinetically-Controlled Ni-Catalyzed Direct Carboxylation of Unactivated Secondary Alkyl Bromides without Chain Walking.

Herein, we report the direct carboxylation of unactivated secondary alkyl bromides enabled by the merger of photoredox and nickel catalysis, a previously inaccessible endeavor in the carboxylation arena. Site-selectivity is dictated by a kinetically controlled insertion of CO2 at the initial C(sp3)-Br site by the rapid formation of Ni(I)-alkyl species, thus avoiding undesired ß-hydride elimination and chain-walking processes. Preliminary mechanistic experiments reveal the subtleties of stereoelectronic effects for guiding the reactivity and site-selectivity.

Understanding the Chemomechanical Function of the Silver-Carbon Interlayer in Sheet-type All-Solid-State Lithium-Metal Batteries.

All-solid-state batteries with lithium metal anodes hold great potential for high-energy battery applications. However, forming and maintaining stable solid-solid contact between the lithium anode and solid electrolyte remains a major challenge. One promising solution is the use of a silver-carbon (Ag-C) interlayer, but its chemomechanical properties and impact on interface stabilities need to be comprehensively explored. Here, we examine the function of Ag-C interlayers in addressing interfacial challenges using various cell configurations. Experiments show that the interlayer improves interfacial mechanical contact, leading to a uniform current distribution and suppressing lithium dendrite growth. Furthermore, the interlayer regulates lithium deposition in the presence of Ag particles via improved Li diffusivity. The sheet-type cells with the interlayer achieve a high energy density of 514.3 Wh L-1 and an average Coulombic efficiency of 99.97% over 500 cycles. This work provides insights into the benefits of using Ag-C interlayers for enhancing the performance of all-solid-state batteries.

Clinical and Immunologic Correlates of Vasodilatory Shock Among Ebola Virus-Infected Nonhuman Primates in a Critical Care Model.

BACKGROUND: Existing models of Ebola virus infection have not fully characterized the pathophysiology of shock in connection with daily virologic, clinical, and immunologic parameters. We implemented a nonhuman primate critical care model to investigate these associations. METHODS: Two rhesus macaques received a target dose of 1000 plaque-forming units of Ebola virus intramuscularly with supportive care initiated on day 3. High-dimensional spectral cytometry was used to phenotype neutrophils and peripheral blood mononuclear cells daily. RESULTS: We observed progressive vasodilatory shock with preserved cardiac function following viremia onset on day 5. Multiorgan dysfunction began on day 6 coincident with the nadir of circulating neutrophils. Consumptive coagulopathy and anemia occurred on days 7 to 8 along with irreversible shock, followed by death. The monocyte repertoire began shifting on day 4 with a decline in classical and expansion of double-negative monocytes. A selective loss of CXCR3-positive B and T cells, expansion of naive B cells, and activation of natural killer cells followed viremia onset. CONCLUSIONS: Our model allows for high-fidelity characterization of the pathophysiology of acute Ebola virus infection with host innate and adaptive immune responses, which may advance host-targeted therapy design and evaluation for use after the onset of multiorgan failure.

Direct Decarboxylation of Trifluoroacetates Enabled by Iron Photocatalysis.

Trifluoroacetates are the most abundant and accessible sources of trifluoromethyl groups, which are key components in pharmaceuticals and agrochemicals. The generation of trifluoromethyl reactive radicals from trifluoroacetates requires their decarboxylation, which is hampered by their high oxidation potential. This constitutes a major challenge for redox-based methods, because of the need to pair the redox potentials with trifluoroacetate. Here we report a strategy based on iron photocatalysis to promote the direct photodecarboxylation of trifluoroacetates that displays reactivity features that escape from redox limitations. Our synthetic design has enabled the use of trifluoroacetates for the trifluoromethylation of more easily oxidizable organic substrates, offering new opportunities for late-stage derivatization campaigns using chemical feedstocks, Earth-abundant catalysts, and visible-light.

Native Spleen Preservation During Visceral Transplantation Inhibits Graft-Versus-Host-Disease Development: Clinical and Experimental Study.

OBJECTIVE: We aimed to assess whether native spleen preservation during visceral transplantation (VT) affects graft-versus-host-disease (GVHD) incidence. SUMMARY BACKGROUND DATA: GVHD is one of the most severe and frequently lethal hematological complications after VT procedures. Because there is no specific treatment for GVHD, it is imperative to develop a strategy to reduce donor lymphocyte engraftment and proliferation. METHODS: Our study included both clinical and experimental data. A total of 108 patients were divided into 3 groups: a native spleen preservation group, a native spleen removal with no donor spleen group, and a donor spleen included (allogeneic spleen) group. We also used an allogeneic VT rat model, in which recipients were divided into 2 groups: a native spleen preservation (+SP) group and a native spleen removal (-S) group. Skin rash appearance, histopathological changes, chimerism, and spleen effects on circulating allogeneic T-cells were assessed. RESULTS: The patients with native spleen preservation showed a lower rate of GVHD ( P <.001) and better survival ( P <.05) than those in the other groups. Skin and histological signs of GVHD were lower in the rats in the +SP group ( P <.05). The donor T-cell frequency in the bloodstream and skin was also significantly reduced when the native spleen was preserved ( P <.01 and P <.0001, respectively). CONCLUSIONS: The clinical and experimental data indicate that recipient spleen preservation protects against GVHD after VT, and donor cell clearance from the bloodstream by spleen macrophages could be the underlying mechanism. Therefore, spleen preservation should be considered in VT procedures, whenever possible.

Novel RNA viruses from the Atlantic Ocean: Ecogenomics, biogeography, and total virioplankton mass contribution from surface to the deep ocean.

Marine viruses play a major role in the energy and nutrient cycle and affect the evolution of their hosts. Despite their importance, there is still little knowledge about RNA viruses. Here, we have explored the Atlantic Ocean, from surface to deep (4.296 m), and used viromics and quantitative methods to unveil the genomics, biogeography, and the mass contribution of RNA viruses to the total viroplankton. A total of 2481 putative RNA viral contigs (>500 bp) and 107 larger bona fide RNA viral genomes (>2.5 kb) were identified; 88 of them representing novel viruses belonging mostly to two clades: Yangshan assemblage (sister clade to the class Alsuviricetes) and Nodaviridae. These viruses were highly endemic and locally abundant, with little or no presence in other oceans since only ≈15% of them were found in at least one of the Tara sampling metatranscriptomes. Quantitative data indicated that the abundance of RNA viruses in the surface and deep chlorophyll maximum zone was within ≈106 VLP/mL representing a potential contribution of 5.2%-24.4% to the total viroplankton community (DNA and RNA viruses), with DNA viruses being the predominant members (≈107 VLP/mL). However, for the deep sample, the observed trend was the opposite, although as further discussed, several biases should be considered. Together these results contribute to our understanding of the diversity, abundance, and distribution of RNA viruses in the oceans and provide a basis for further investigation into their ecological roles and biogeography.

Nailfold videocapillaroscopy patterns in systemic sclerosis: implications for cutaneous subsets, disease features and prognostic value for survival.

OBJECTIVES: To assess the associations and prognostic value of scleroderma patterns by nailfold videocapillaroscopy (NVC) in patients with systemic sclerosis (SSc) and cutaneous subsets. METHODS: At baseline, 1356 SSc patients from the RESCLE registry were compared according to the scleroderma pattern as Late pattern and non-Late pattern, which included Early and Active patterns. Patient characteristics, disease features, survival time and causes of death were analysed. RESULTS: Late pattern was identified in 540 (39.8%), and non-Late pattern in 816 (60.2%) patients (88% women; 987 lcSSc/251 dcSSc). Late pattern was associated to dcSSc (OR=1.96; p<0.001), interstitial lung disease (ILD) (OR=1.29; p=0.031), and scleroderma renal crisis (OR=3.46; p<0.001). Once the cutaneous subset was disregarded in an alternative analysis, both digital ulcers (DU) (OR=1.29; p<0.037) and anti-topoisomerase I antibodies (OR=1.39; p< 0.036) emerged associated with the Late pattern. By cutaneous subsets, associations with Late pattern were: (1) in dcSSc, acro-osteolysis (OR=2.13; p=0.022), and systolic pulmonary artery pressure >40 mmHg by Doppler echocardiogram (OR=2.24; p<0.001); and (2) in lcSSc, ILD (OR=1.38; p=0.028). Survival was reduced in dcSSc with Late pattern compared to non-Late pattern (p=0.049). Risk factors for SSc mortality in multivariate regression Cox analysis were age at diagnosis (HR=1.03; p<0.001), dcSSc (HR=2.48; p<0.001), DU (HR=1.38; p=0.046), ILD (HR=2.81; p<0.001), and pulmonary arterial hypertension (HR=1.99; p<0.001). CONCLUSIONS: SSc patients with Late pattern more frequently present dcSSc and develop more fibrotic and vascular manifestations. Advanced microangiopathy by NVC identifies dcSSc patients at risk of reduced survival due to SSc-related causes.

Preclinical Study of DCD and Normothermic Perfusion for Visceral Transplantation.

Considering recent clinical and experimental evidence, expectations for using DCD-derived intestines have increased considerably. However, more knowledge about DCD procedure and long-term results after intestinal transplantation (ITx) is needed. We aimed to describe in detail a DCD procedure for ITx using normothermic regional perfusion (NRP) in a preclinical model. Small bowel was obtained from pigs donors after 1 h of NRP and transplanted to the recipients. Graft Intestinal samples were obtained during the procedure and after transplantation. Ischemia-reperfusion injury (Park-Chiu score), graft rejection and transplanted intestines absorptive function were evaluated. Seven of 8 DCD procedures with NRP and ITx were successful (87.5%), with a good graft reperfusion and an excellent recovery of the recipient. The architecture of grafts was well conserved during NRP. After an initial damage of Park-chiu score of 4, all grafts recovered from ischemia-reperfusion, with no or very subtle alterations 2 days after ITx. Most recipients (71.5%) did not show signs of rejection. Only two cases demonstrated histologic signs of mild rejection 7 days after ITx. Interestingly intestinal grafts showed good absorptive capacity. The study's results support the viability of intestinal grafts from DCD using NRP, contributing more evidence for the use of DCD for ITx.

Remote carboxylation of halogenated aliphatic hydrocarbons with carbon dioxide.

Catalytic carbon-carbon bond formation has enabled the streamlining of synthetic routes when assembling complex molecules. It is particularly important when incorporating saturated hydrocarbons, which are common motifs in petrochemicals and biologically relevant molecules. However, cross-coupling methods that involve alkyl electrophiles result in catalytic bond formation only at specific and previously functionalized sites. Here we describe a catalytic method that is capable of promoting carboxylation reactions at remote and unfunctionalized aliphatic sites with carbon dioxide at atmospheric pressure. The reaction occurs via selective migration of the catalyst along the hydrocarbon side-chain with excellent regio- and chemoselectivity, representing a remarkable reactivity relay when compared with classical cross-coupling reactions. Our results demonstrate that site-selectivity can be switched and controlled, enabling the functionalization of less-reactive positions in the presence of a priori more reactive ones. Furthermore, we show that raw materials obtained in bulk from petroleum processing, such as alkanes and unrefined mixtures of olefins, can be used as substrates. This offers an opportunity to integrate a catalytic platform en route to valuable fatty acids by transforming petroleum-derived feedstocks directly.

Hyperspectral camera as a compact payload architecture for remote sensing applications.

Monitoring and observation over the surface of the Earth have been a matter of global interest. In this path, recent efforts aim to develop a spatial mission to perform remote sensing applications. Mainly, CubeSat nanosatellites have emerged as a standard for developing low-weight and small-sized instruments. In terms of payloads, state-of-the-art optical systems for CubeSats are expensive and designed to work in general use cases. To overcome these limitations, this paper presents a 1.4 U compact optical system to acquire spectral images from a CubeSat standard satellite at the height of 550 km. To validate the proposed architecture, optical simulations using ray tracing simulation software are presented. Because the performance of computer vision tasks is highly related to data quality, we compared the optical system in terms of the classification performance on a real remote sensing application. The performances of the optical characterization and land cover classification show that the proposed optical system achieves a compact instrument, operating at a spectral range from 450 nm to 900 nm discretized on 35 spectral bands. The optical system has an overall f-number of 3.41 with a ground sampling distance of 52.8 m and a swath of 40 km. Additionally, the design parameters for each optical element are publicly available for validation, repeatability, and reproducibility of the results.

Identification of Pre-Renal and Intrinsic Acute Kidney Injury by Anamnestic and Biochemical Criteria: Distinct Association with Urinary Injury Biomarkers.

Acute kidney injury (AKI) is a syndrome of sudden renal excretory dysfunction with severe health consequences. AKI etiology influences prognosis, with pre-renal showing a more favorable evolution than intrinsic AKI. Because the international diagnostic criteria (i.e., based on plasma creatinine) provide no etiological distinction, anamnestic and additional biochemical criteria complement AKI diagnosis. Traditional, etiology-defining biochemical parameters, including the fractional excretion of sodium, the urinary-to-plasma creatinine ratio and the renal failure index are individually limited by confounding factors such as diuretics. To minimize distortion, we generated a composite biochemical criterion based on the congruency of at least two of the three biochemical ratios. Patients showing at least two ratios indicative of intrinsic AKI were classified within this category, and those with at least two pre-renal ratios were considered as pre-renal AKI patients. In this study, we demonstrate that the identification of intrinsic AKI by a collection of urinary injury biomarkers reflective of tubular damage, including NGAL and KIM-1, more closely and robustly coincide with the biochemical than with the anamnestic classification. Because there is no gold standard method for the etiological classification of AKI, the mutual reinforcement provided by the biochemical criterion and urinary biomarkers supports an etiological diagnosis based on objective diagnostic parameters.

The economics impacts of long-run droughts: Challenges, gaps, and way forward.

Quantifying drought's economic impacts has been key for decision-making to build future strategies and improve the development and implementation of proactive plans. However, climate change is changing drought frequency, intensity, and durability. These changes imply modifications of their economic impact, as longer droughts result in greater cumulative economic losses for water users. Though the longer the drought lasts, other factors also play a crucial role in its economic outcomes, such as Infrastructure capacity (IC), the Amount of Water in Storage (AWS) in reservoirs and aquifers, and short- and long-term responses to it. This study proposes and applies an analytical framework for the economic assessment of long-run droughts, assessing and explaining central Chile megadrought economic effects through the factors that begin to influence the economic impact level in this setting. High levels of both IC and the AWS, as well as short- and long-term responses of water users, allow for high resilience to long-run droughts, tolerating extraordinary water disruption in its society with relatively low total economic impacts. Despite this adaptability, long-term droughts bring places to a water-critical threshold where long-term adaptation strategies may be less flexible than short-term strategies, escalating the adverse economic effects. This fact suggests that the economic evaluation of megadrought needs to focus on future tipping points (substantial water scarcity). The tipping point depends on the IC, how water users manage the AWS, and adaptation strategies. Establishing the tipping point should be a priority for future interdisciplinary research.

Asynchronous electronic consultation between primary care and specialized care proved effective for continuum of care for viraemic hepatitis C patients.

INTRODUCTION: It has been proposed that primary care diagnose and treat hepatitis C virus (HCV) infection. However, a care circuit between primary and specialized care based on electronic consultation (EC) can be just as efficient in the micro-elimination of HCV. It is proposed to study characteristics and predictive factors of continuity of care in a circuit between primary and specialized care. METHODS: From February/2018 to December/2019, all EC between primary and specialized care were evaluated and those due to HCV were identified. Variables for regression analysis and to identify predictors of completing the care cascade were recorded. RESULTS: From 8098 EC, 138 were performed by 89 (29%) general practitioners over 118 patients (median 50.8 years; 74.6% men) and were related to HCV (1.9%). Ninety-two patients (78%) were diagnosed>6 months ago, and 26.3% met criteria for late presentation. Overall, 105 patients required assessment by the hepatologist, 82% (n=86) presented for the appointment, of which 67.6% (n=71) were viraemic, 98.6% of known. Finally, 61.9% (n=65) started treatment. Late-presenting status was identified as an independent predictor to complete the care cascade (OR 1.93, CI 1.71-1.99, p<0.001). CONCLUSION: Communication pathway between Primary and Specialized Care based on EC is effective in avoiding significant losses of viraemic patients. However, the referral rate is very low, high in late-stage diagnoses, heterogeneous, and low in new diagnoses. Therefore, early detection strategies for HCV infection in primary care are urgently needed.

Integration of Highly Luminescent Lead Halide Perovskite Nanocrystals on Transparent Lead Halide Nanowire Waveguides through Morphological Transformation and Spontaneous Growth in Water.

The integration of highly luminescent CsPbBr3 quantum dots on nanowire waveguides has enormous potential applications in nanophotonics, optical sensing, and quantum communications. On the other hand, CsPb2 Br5 nanowires have also attracted a lot of attention due to their unique water stability and controversial luminescent property. Here, the growth of CsPbBr3 nanocrystals on CsPb2 Br5 nanowires is reported first by simply immersing CsPbBr3 powder into pure water, CsPbBr3- γ Xγ (X = Cl, I) nanocrystals on CsPb2 Br5 -γ Xγ nanowires are then synthesized for tunable light sources. Systematic structure and morphology studies, including in situ monitoring, reveal that CsPbBr3 powder is first converted to CsPb2 Br5 microplatelets in water, followed by morphological transformation from CsPb2 Br5 microplatelets to nanowires, which is a kinetic dissolution-recrystallization process controlled by electrolytic dissociation and supersaturation of CsPb2 Br5 . CsPbBr3 nanocrystals are spontaneously formed on CsPb2 Br5 nanowires when nanowires are collected from the aqueous solution. Raman spectroscopy, combined photoluminescence, and SEM imaging confirm that the bright emission originates from CsPbBr3 -γ Xγ nanocrystals while CsPb2 Br5 -γ Xγ nanowires are transparent waveguides. The intimate integration of nanoscale light sources with a nanowire waveguide is demonstrated through the observation of the wave guiding of light from nanocrystals and Fabry-Perot interference modes of the nanowire cavity.

First multivisceral transplantation in Mitchell-Riley/Martinez-Frias syndrome.

BACKGROUND: MRS/MFS is a rare multisystem disorder with a poor prognosis. The high mortality rate of this syndrome is related to the severity of the associated gastrointestinal, pancreatic, and hepatobiliary conditions, as most of them are not amenable to conventional medical and surgical treatments. METHODS: We report the case of a Romani girl with all the key clinical features of MRS/MFS, and a review of cases reported in the literature. Our patient is a newborn from consanguineous parents who presented duodenal atresia, hypoplastic pancreas, gallbladder agenesis, and neonatal diabetes. Given the clinical suspicion of MRS/MFS, a genetic analysis was performed which revealed the presence of a homozygous variant in the RFX6 gene. During the course of the disease, the patient presented intractable secretory diarrhea and severe intestinal failure. RESULTS: At 2 years of age, she underwent MVT of the stomach, duodenum, small intestine, colon, liver, and pancreas. There were no surgical complications. Histologic evaluation of the small bowel showed extensive patches of gastric heterotopia. After more than 10 years of follow-up, she had presented with normal gastrointestinal, hepatic, and pancreatic function. She has one of the longest survival periods in the literature. CONCLUSIONS: Our experience suggests that multivisceral transplantation may be a promising option in select cases of MRS/MFS.

The impact of nutritive and non-nutritive sweeteners on the central nervous system: preliminary study.

BACKGROUND: Human consumption of food and beverages containing added nutritive or non-nutritive sweeteners has increased worldwide. OBJECTIVE: The present study evaluated the possible impact of frequent sweetener consumption on human CNS activity and functions through neuropsychological testing and EEG/qEEG analysis. METHODS: A sample of 23 women and 16 men, aged 18-35, with a body mass index between 18 and 24.9 kg/m2 was evaluated. Participants underwent a 1-week washout period in which food with added sugars or sweeteners was restricted from their diet. Initial assessment of cognitive functions was performed with a validated neuropsychological test and EEG/qEEG analysis, prior to supplementation. Sucrose, sucralose, or steviol glycosides, in commercially available presentations, were randomly assigned to three experimental groups of 13 participants each. Sweeteners were supplemented in fixed amounts, daily, for six weeks. After supplementation, neurological tests were repeated and the initial and final results were compared. RESULTS: The results show no significant changes between final and initial measures in the steviol glycosides group. However, a significant decrease in encoding memory was found in the sucrose group in the final evaluation. Strikingly, the sucralose group showed a significant decrease in overall memory, encoding memory, and executive functions after supplementation. Furthermore, qEEG analysis showed an increase in theta wave absolute and relative power at the final evaluation in the same group. CONCLUSION: These data show that frequent consumption of specific sweeteners is accompanied by measurable changes in EEG/qEEG activity and neuropsychological test performance in humans.

The Urinary Level of Injury Biomarkers Is Not Univocally Reflective of the Extent of Toxic Renal Tubular Injury in Rats.

Nephrotoxicity is a major cause of intrinsic acute kidney injury (AKI). Because renal tissue damage may occur independently of a reduction in glomerular filtration rate and of elevations in plasma creatinine concentration, so-called injury biomarkers have been proposed to form part of diagnostic criteria as reflective of tubular damage independently of renal function status. We studied whether the urinary level of NGAL, KIM-1, GM2AP, t-gelsolin, and REGIIIb informed on the extent of tubular damage in rat models of nephrotoxicity, regardless of the etiology, moment of observation, and underlying pathophysiology. At a time of overt AKI, urinary biomarkers were measured by Western blot or ELISA, and tubular necrosis was scored from histological specimens stained with hematoxylin and eosin. Correlation and regression studies revealed that only weak relations existed between biomarkers and tubular damage. Due to high interindividual variability in the extent of damage for any given biomarker level, urinary injury biomarkers did not necessarily reflect the extent of the underlying tissue injury in individual rats. We contended, in this work, that further pathophysiological contextualization is necessary to understand the diagnostic significance of injury biomarkers before they can be used for renal tubular damage severity stratification in the context of nephrotoxic and, in general, intrinsic AKI.

Protective Effect of Quercetin 3-O-Glucuronide against Cisplatin Cytotoxicity in Renal Tubular Cells.

Quercetin, a flavonoid with promising therapeutic potential, has been shown to protect from cisplatin nephrotoxicity in rats following intraperitoneal injection, but its low bioavailability curtails its prospective clinical utility in oral therapy. We recently developed a micellar formulation (P-quercetin) with enhanced solubility and bioavailability, and identical nephroprotective properties. As a first aim, we herein evaluated the oral treatment with P-quercetin in rats, which displayed no nephroprotection. In order to unravel this discrepancy, quercetin and its main metabolites were measured by HPLC in the blood and urine after intraperitoneal and oral administrations. Whilst quercetin was absorbed similarly, the profile of its metabolites was different, which led us to hypothesize that nephroprotection might be exerted in vivo by a metabolic derivate. Consequently, we then aimed to evaluate the cytoprotective capacity of quercetin and its main metabolites (quercetin 3-O-glucoside, rutin, tamarixetin, isorhamnetin and quercetin 3-O-glucuronide) against cisplatin toxicity, in HK-2 and NRK-52E tubular cell lines. Cells were incubated for 6 h with quercetin, its metabolites or vehicle (pretreatment), and subsequently 18 h in cotreatment with 10-300 µM cisplatin. Immediately after treatment, cell cultures were subject to the MTT technique as an index of cytotoxicity and photographed under light microscopy for phenotypic assessment. Quercetin afforded no direct cytoprotection and quercetin-3-O-glucuronide was the only metabolite partially preventing the effect of cisplatin in cultured tubule cells. Our results identify a metabolic derivative of quercetin contributing to its nephroprotection and prompt to further explore exogenous quercetin-3-O-glucuronide in the prophylaxis of tubular nephrotoxicity.